General information for g11384.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Chondroitin sulfate synthase 1.
Parent gene
- The parent gene g11384 is located on chr_1: 15889093..15890377 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g11384 | g11384.t3 | TSS | g11384.t3 | 15884879 | 15884879 |
| chr_1 | g11384 | g11384.t3 | isoform | g11384.t3 | 15885206 | 15886640 |
| chr_1 | g11384 | g11384.t3 | exon | g11384.t3.exon1 | 15885206 | 15885347 |
| chr_1 | g11384 | g11384.t3 | cds | g11384.t3.CDS1 | 15885206 | 15885347 |
| chr_1 | g11384 | g11384.t3 | exon | g11384.t3.exon2 | 15886028 | 15886216 |
| chr_1 | g11384 | g11384.t3 | cds | g11384.t3.CDS2 | 15886028 | 15886216 |
| chr_1 | g11384 | g11384.t3 | exon | g11384.t3.exon3 | 15886453 | 15886640 |
| chr_1 | g11384 | g11384.t3 | cds | g11384.t3.CDS3 | 15886453 | 15886640 |
| chr_1 | g11384 | g11384.t3 | TTS | g11384.t3 | NA | NA |
Sequences
>g11384.t3 Gene=g11384 Length=519
ATGACACAACACTTAAAACTTTTTTATGGTCTTTTGGGAGCTGTGATAGGATTATGTATT
GGGACTTTTCTCAAAAGTTTCAATACTATGGAGACAATTACACAGTGCGACCTGTTGTCT
GCCGCAAGTGTTCAATTGAAATCACCATTACAATTAATTAATTTAACGGATGAAGAGACC
CCAGTAAACAGTCAACGAACATTGGTTTTTGTCGGCGTAATGACATCCAAAGACTTCTTA
GAATCGCGTGCAAAGTCTGTGTATAATACATGGGGTAAATCAGTTCCTGGAAGGATTGCT
TTCTTTAGTTCTGAAGGCTCAGCTATGGATGATCTTCCAGTTATTGCGCTTAATGGTGTT
GACGATCGTTATCCGCCACAACGTAAATCATTTACGATGCTACACTACATGTATGAACAT
TATATTGACAAATTCGAATGGTTTCTTCGTGCTGATGATGATGTTTTTATTAAGACGGAT
AAACTCGAAAAGTTTTTAAGACGTATCGACTCAACAAAG
>g11384.t3 Gene=g11384 Length=173
MTQHLKLFYGLLGAVIGLCIGTFLKSFNTMETITQCDLLSAASVQLKSPLQLINLTDEET
PVNSQRTLVFVGVMTSKDFLESRAKSVYNTWGKSVPGRIAFFSSEGSAMDDLPVIALNGV
DDRYPPQRKSFTMLHYMYEHYIDKFEWFLRADDDVFIKTDKLEKFLRRIDSTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11384.t3 | Gene3D | G3DSA:3.90.550.50 | - | 56 | 173 | 4.5E-13 |
| 2 | g11384.t3 | PANTHER | PTHR12369 | CHONDROITIN SYNTHASE | 3 | 173 | 2.9E-57 |
| 3 | g11384.t3 | PANTHER | PTHR12369:SF11 | HEXOSYLTRANSFERASE | 3 | 173 | 2.9E-57 |
| 1 | g11384.t3 | Pfam | PF02434 | Fringe-like | 68 | 172 | 4.2E-7 |
| 6 | g11384.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 6 | - |
| 8 | g11384.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 27 | - |
| 7 | g11384.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 28 | 173 | - |
| 4 | g11384.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 24 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0016757 | glycosyltransferase activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
